i just have a 2.5" muffler. the rest of the system is still 2.25". if you go with a full exhaust system, stick with 2.25". i only have a 2.5" muffler because it was free
muffler has no effect on emissions at all. just don't mess with the cat. 2.5 would be the biggest i would recommend, unless you do major mods, like a turbo. 2.25 will keep the stock powerband, while the 2.5 will loose some low end, but you will gain a little top end.